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- PDB-3oni: Crystal Structure of the second bromodomain of human BRD2 in comp... -

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Basic information

Entry
Database: PDB / ID: 3oni
TitleCrystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor JQ1
ComponentsBromodomain containing 2, isoform CRA_a
KeywordsCELL CYCLE / Structural Genomics / Structural Genomics Consortium / SGC / Bromodomain / Inhibition / Probe
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / 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 ...chromatin looping / acetylation-dependent protein binding / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JQ1 / NICKEL (II) ION / Bromodomain-containing protein 2 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bradner, J.E. / Structural Genomics Consortium (SGC)
CitationJournal: Nature / Year: 2010
Title: Selective inhibition of BET bromodomains.
Authors: Filippakopoulos, P. / Qi, J. / Picaud, S. / Shen, Y. / Smith, W.B. / Fedorov, O. / Morse, E.M. / Keates, T. / Hickman, T.T. / Felletar, I. / Philpott, M. / Munro, S. / McKeown, M.R. / Wang, ...Authors: Filippakopoulos, P. / Qi, J. / Picaud, S. / Shen, Y. / Smith, W.B. / Fedorov, O. / Morse, E.M. / Keates, T. / Hickman, T.T. / Felletar, I. / Philpott, M. / Munro, S. / McKeown, M.R. / Wang, Y. / Christie, A.L. / West, N. / Cameron, M.J. / Schwartz, B. / Heightman, T.D. / La Thangue, N. / French, C.A. / Wiest, O. / Kung, A.L. / Knapp, S. / Bradner, J.E.
History
DepositionAug 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain containing 2, isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0756
Polymers13,3751
Non-polymers7005
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bromodomain containing 2, isoform CRA_a
hetero molecules

A: Bromodomain containing 2, isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,15012
Polymers26,7512
Non-polymers1,39910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2060 Å2
ΔGint-25 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 71.710, 31.970
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-456-

NI

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Components

#1: Protein Bromodomain containing 2, isoform CRA_a / Putative uncharacterized protein DKFZp313H139


Mass: 13375.410 Da / Num. of mol.: 1 / Fragment: residues 224-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, DKFZp313H139, hCG_17503 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q658Y7, UniProt: P25440*PLUS
#2: Chemical ChemComp-JQ1 / (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium / JQ1


Mass: 457.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26ClN4O2S / Comment: inhibitor*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% Jeffamine600, 0.5M CsCl, 5% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 10 / Number: 54515 / Rsym value: 0.055 / D res high: 1.609 Å / D res low: 27.32 Å / Num. obs: 16213 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.0927.3298.810.0310.0313.2
3.65.0910010.0320.0323.4
2.943.610010.040.043.5
2.552.9410010.0450.0453.5
2.282.5510010.050.053.5
2.082.2810010.060.063.4
1.922.0810010.0850.0853.4
1.81.9210010.1250.1253.4
1.71.810010.1790.1793.3
1.611.79710.240.243.1
ReflectionResolution: 1.61→29.16 Å / Num. all: 16295 / Num. obs: 16213 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.61-1.73.10.242.6700822480.2497
1.7-1.83.30.1793.6734222000.179100
1.8-1.923.40.1255.3707420970.125100
1.92-2.083.40.0857.7658319300.085100
2.08-2.283.40.0611624118150.06100
2.28-2.553.50.0513.2565216380.05100
2.55-2.943.50.04514.3505214580.045100
2.94-3.63.50.0414.7431912500.04100
3.6-5.093.40.03217.333729870.032100
5.09-27.323.20.03116.518725900.03198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.32 Å
Translation2.5 Å27.32 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

3hmh

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 1.61→29.16 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1778 / WRfactor Rwork: 0.145 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9219 / SU B: 1.988 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0793 / SU Rfree: 0.0822 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 829 5.1 %RANDOM
Rwork0.1485 ---
all0.1502 16272 --
obs0.1502 16171 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.26 Å2 / Biso mean: 13.0347 Å2 / Biso min: 4.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.61→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 41 174 1118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022989
X-RAY DIFFRACTIONr_bond_other_d0.0010.02691
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9951335
X-RAY DIFFRACTIONr_angle_other_deg1.5293.0011665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0615109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10823.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25415174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.234157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_mcbond_it1.7393558
X-RAY DIFFRACTIONr_mcbond_other0.5283215
X-RAY DIFFRACTIONr_mcangle_it2.9055902
X-RAY DIFFRACTIONr_scbond_it4.7548431
X-RAY DIFFRACTIONr_scangle_it6.72911433
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 64 -
Rwork0.314 1007 -
all-1071 -
obs--92.33 %
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)
10.30310.2146-0.08960.7529-0.08410.0543-0.003-0.0079-0.00260.01510.0004-0.02420.00970.02250.00270.0320.00090.00120.0325-0.00110.027540.348633.308-1.4524
20.4282-0.14870.24940.1594-0.26531.43150.0127-0.00720.04780.0535-0.03180.01230.07730.02080.0190.06-0.00280.00040.0251-0.00050.018836.140728.63339.6268
30.70590.06950.02420.411-0.20830.01330.00280.0139-0.001-0.02390.01390.01930.00590.0002-0.01670.0408-0.00370.00210.0317-0.00050.027531.684935.1712-5.6671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A346 - 399
2X-RAY DIFFRACTION2A400 - 417
3X-RAY DIFFRACTION3A418 - 455

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