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- PDB-3s91: Crystal Structure of the first bromodomain of human BRD3 in compl... -

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Basic information

Entry
Database: PDB / ID: 3s91
TitleCrystal Structure of the first bromodomain of human BRD3 in complex with the inhibitor JQ1
ComponentsBromodomain-containing protein 3
KeywordsUNKNOWN FUNCTION / BRD3 / Bromodomain containing protein 3 / ORFX / RING3 like gene / RING3L / JQ1 / Structural Genomics / Structural Genomics Consortium / SGC
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-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
ISOPROPYL ALCOHOL / Chem-JQ1 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Qi, J. / Keates, T. / Felletar, I. / Fedorov, O. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Filippakopoulos, P. / Picaud, S. / Qi, J. / Keates, T. / Felletar, I. / Fedorov, O. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bradner, J.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the first bromodomain of human BRD3 in complex with the inhibitor JQ1
Authors: Filippakopoulos, P. / Picaud, S. / Qi, J. / Keates, T. / Felletar, I. / Fedorov, O. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Bradner, J.E. / Knapp, S.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1053
Polymers14,5871
Non-polymers5182
Water1,33374
1
A: Bromodomain-containing protein 3
hetero molecules

A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2106
Polymers29,1742
Non-polymers1,0364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1960 Å2
ΔGint-8 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.560, 86.560, 76.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-173-

HOH

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Components

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


Mass: 14586.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q15059
#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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 14% isopropanol, 0.14M CaCl2, 30% glycerol, 0.7M acetate, pH 4.6, 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: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 7.7 / Number: 61487 / Rsym value: 0.097 / D res high: 2.06 Å / D res low: 28.743 Å / Num. obs: 11011 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.5128.7498.910.020.024.9
4.616.5110010.0340.0345.4
3.764.6110010.0370.0375.6
3.263.7610010.0620.0625.7
2.913.2610010.1130.1135.7
2.662.9110010.1780.1785.7
2.462.6610010.3010.3015.7
2.32.4610010.430.435.7
2.172.310010.6120.6125.7
2.062.1799.910.8090.8095.2
ReflectionResolution: 2.06→28.743 Å / Num. all: 11022 / Num. obs: 11011 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.06-2.175.20.8091802015520.80999.9
2.17-2.35.70.6121.3843214800.612100
2.3-2.465.70.431.8808514130.43100
2.46-2.665.70.3012.6742112930.301100
2.66-2.915.70.1784.4696312180.178100
2.91-3.265.70.1136.9638911160.113100
3.26-3.765.70.0621256399890.062100
3.76-4.615.60.03719.447868490.037100
4.61-6.515.40.03421.837386890.034100
6.51-28.7434.90.0231.220144120.0298.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.74 Å
Translation2.5 Å28.74 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: PDB entry 2NXB

2nxb


Resolution: 2.06→28.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1906 / WRfactor Rwork: 0.1622 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8489 / SU B: 8.009 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1596 / SU Rfree: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 526 4.8 %RANDOM
Rwork0.195 ---
all0.1968 10990 --
obs0.1968 10985 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.3 Å2 / Biso mean: 37.3817 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.84 Å20 Å2
2--1.69 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.06→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 35 74 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022946
X-RAY DIFFRACTIONr_bond_other_d0.0010.02607
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9781291
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0011481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4275106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78825.68244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08815157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.667151
X-RAY DIFFRACTIONr_chiral_restr0.0830.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 41 -
Rwork0.308 738 -
all-779 -
obs--99.49 %
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)
13.93040.52480.24582.6743-0.61486.07470.158-0.01770.17550.1501-0.2313-0.0779-0.4006-0.12580.07340.0955-0.0064-0.01850.02710.01350.050134.74778.889110.7011
26.911-3.2912.44433.5916-0.49196.04950.0109-0.03410.1390.1095-0.0602-0.1052-0.2738-0.09320.04930.0508-0.0134-0.01810.01990.02520.041833.45778.64234.0606
316.71231.84597.56763.2111.405216.82880.0358-0.08250.02340.2251-0.11030.34240.5297-1.64730.07450.114-0.09450.0020.2062-0.00050.054726.4106-1.52447.7978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 77
2X-RAY DIFFRACTION2A78 - 123
3X-RAY DIFFRACTION3A124 - 142

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