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

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Basic information

Entry
Database: PDB / ID: 3uvw
TitleCrystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac)
Components
  • Bromodomain-containing protein 4BRD4
  • Histone H4
KeywordsTRANSCRIPTION/PROTEIN BINDING / Bromodomain / Bromodomain containing protein 4 / CAP / HUNK1 / MCAP / Mitotic chromosome associated protein / peptide complex / Structural Genomics Consortium / SGC / PROTEIN BINDING / TRANSCRIPTION / TRANSCRIPTION-PROTEIN BINDING complex
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 / negative regulation of megakaryocyte differentiation / positive regulation of T-helper 17 cell lineage commitment / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / negative regulation of megakaryocyte differentiation / positive regulation of T-helper 17 cell lineage commitment / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / telomere organization / histone reader activity / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / RNA polymerase II CTD heptapeptide repeat kinase activity / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / condensed nuclear chromosome / Defective pyroptosis / HDACs deacetylate histones / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of canonical NF-kappaB signal transduction / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / 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 / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H4, conserved site / Histone H4 signature. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsFilippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3833
Polymers16,3212
Non-polymers621
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-10 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.500, 47.280, 59.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsMonomer

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: unp residues 44-168
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: Protein/peptide Histone H4 / / Peptide (H4K5acK8ac)


Mass: 1221.347 Da / Num. of mol.: 1 / Fragment: unp residues 2-12 / Source method: obtained synthetically
Details: Human Histone 4 peptide (Uniprot: P62805) residues 1-11 acetylated on K5 and K8
Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.83 Å3/Da / Density % sol: 32.87 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Av σ(I) over netI: 4.3 / Number: 141841 / Rsym value: 0.1 / D res high: 1.37 Å / D res low: 34.59 Å / Num. obs: 25818 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
4.3334.5999.510.0680.0685.7
3.064.3399.810.0760.0765.5
2.53.0610010.0860.0865.9
2.172.510010.0830.0836.1
1.942.1710010.0970.0976.1
1.771.9410010.1260.1266.2
1.641.7710010.1810.1816.2
1.531.6410010.260.266.2
1.441.5310010.3780.3784.9
1.371.4497.210.520.523.1
ReflectionResolution: 1.37→37.01 Å / Num. all: 25922 / Num. obs: 25818 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.37-1.443.10.521.51121136170.5297.2
1.44-1.534.90.37821746835430.378100
1.53-1.646.20.262.92059433190.26100
1.64-1.776.20.1814.11922631020.181100
1.77-1.946.20.1265.51763628540.126100
1.94-2.176.10.0976.51600926060.097100
2.17-2.56.10.0837.11407723200.083100
2.5-3.065.90.0866.71172619760.086100
3.06-4.335.50.0767.2864415620.07699.8
4.33-34.595.70.0687.852509190.06899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.84 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.59 Å
Translation2.5 Å34.59 Å

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Processing

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

2oss

2ouo

2grc

2oo1

3dai

3d7c


Resolution: 1.37→37.01 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1693 / WRfactor Rwork: 0.1235 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9171 / SU B: 1.864 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0606 / SU Rfree: 0.0575 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 1312 5.1 %RANDOM
Rwork0.1246 ---
all0.1269 25894 --
obs0.1269 25770 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.55 Å2 / Biso mean: 14.0345 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.37→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 4 223 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221232
X-RAY DIFFRACTIONr_bond_other_d0.0020.02863
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9961678
X-RAY DIFFRACTIONr_angle_other_deg1.64532139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12125.34558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19615221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.141155
X-RAY DIFFRACTIONr_chiral_restr0.1110.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211338
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02226
X-RAY DIFFRACTIONr_mcbond_it3.4893726
X-RAY DIFFRACTIONr_mcbond_other2.0673280
X-RAY DIFFRACTIONr_mcangle_it4.551189
X-RAY DIFFRACTIONr_scbond_it5.8978506
X-RAY DIFFRACTIONr_scangle_it8.00411479
X-RAY DIFFRACTIONr_rigid_bond_restr2.81532095
X-RAY DIFFRACTIONr_sphericity_free13.0673223
X-RAY DIFFRACTIONr_sphericity_bonded5.18832059
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 77 -
Rwork0.274 1732 -
all-1809 -
obs--94.66 %

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