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- PDB-3svg: Crystal Structure of the first bromodomain of human BRD4 in compl... -

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Basic information

Entry
Database: PDB / ID: 3svg
TitleCrystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand
ComponentsBromodomain-containing protein 4
KeywordsUNKNOWN FUNCTION / Isoxazole / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / 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-ODR / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / Hewings, S.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Conway, S.J. ...Filippakopoulos, P. / Picaud, S. / Felletar, I. / Hewings, S.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Conway, S.J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand
Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / Hewings, S.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Conway, S.J. / Knapp, S.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5475
Polymers15,0991
Non-polymers4484
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.660, 44.190, 77.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ODR / (1R)-1-[3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-ethoxyphenyl]ethanol


Mass: 261.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Na2SO4, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 8.5, 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: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Av σ(I) over netI: 9.3 / Number: 67890 / Rsym value: 0.067 / D res high: 1.68 Å / D res low: 25.95 Å / Num. obs: 15429 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.3125.959910.0260.0264.1
3.765.3110010.0240.0244.5
3.073.7610010.0390.0394.6
2.663.0710010.0530.0534.6
2.382.6610010.0750.0754.6
2.172.3810010.1020.1024.5
2.012.1710010.1460.1464.5
1.882.0110010.2370.2374.5
1.771.8810010.3820.3824.4
1.681.779910.580.583.8
ReflectionResolution: 1.68→25.95 Å / Num. all: 15460 / Num. obs: 15429 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.68-1.773.80.581.3842922070.5899
1.77-1.884.40.3822927120860.382100
1.88-2.014.50.2373.2882619690.237100
2.01-2.174.50.1465.2833018440.146100
2.17-2.384.50.1027.3771316990.102100
2.38-2.664.60.0759.9707715510.075100
2.66-3.074.60.05313.6634113820.053100
3.07-3.764.60.03917.1542011910.039100
3.76-5.314.50.02420.242199430.024100
5.31-25.954.10.02614.322645570.02699

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.86 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.08 Å
Translation2.5 Å23.08 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 2OSS

2oss


Resolution: 1.68→25.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1941 / WRfactor Rwork: 0.1569 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8721 / SU B: 3.948 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1075 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 767 5 %RANDOM
Rwork0.1756 ---
all0.1776 15411 --
obs0.1776 15383 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.48 Å2 / Biso mean: 19.6267 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.65 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.68→25.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 31 125 1208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221146
X-RAY DIFFRACTIONr_bond_other_d0.0010.02792
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9931563
X-RAY DIFFRACTIONr_angle_other_deg0.9533.0011941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1695136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35525.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65315201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.411154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02205
X-RAY DIFFRACTIONr_mcbond_it2.7913659
X-RAY DIFFRACTIONr_mcbond_other0.873248
X-RAY DIFFRACTIONr_mcangle_it4.13551090
X-RAY DIFFRACTIONr_scbond_it5.4728487
X-RAY DIFFRACTIONr_scangle_it7.38811468
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 61 -
Rwork0.457 1043 -
all-1104 -
obs--97.87 %
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)
10.35930.11760.06231.11251.28350.94870.0222-0.0393-0.0203-0.0255-0.09980.0138-0.01580.01180.07770.0678-0.0097-0.01610.0520.01330.023932.811620.797620.5355
20.1812-0.14460.07530.81450.10530.2797-0.03940.01130.00290.03280.0204-0.0199-0.0291-0.00940.0190.03920.0002-0.00950.040.00140.035530.837124.91046.5086
30.08430.9349-0.87827.05422.71983.5525-0.010.07430.15240.21970.10310.1154-0.28620.1149-0.09310.1070.0274-0.01110.00640.0160.051729.941941.92119.4666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 59
2X-RAY DIFFRACTION2A60 - 157
3X-RAY DIFFRACTION3A158 - 168

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