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- PDB-3uw9: Crystal Structure of the first bromodomain of human BRD4 in compl... -

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Entry
Database: PDB / ID: 3uw9
TitleCrystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac)
Components
  • Bromodomain-containing protein 4
  • histone 4 peptide (H4K8acK12ac)
KeywordsPROTEIN BINDING / Bromodomain / Bromodomain containing protein 4 / CAP / HUNK1 / MCAP / Mitotic chromosome associated protein / peptide complex / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / negative regulation of megakaryocyte differentiation / 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / transcription coregulator activity / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / positive regulation of transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / p53 binding / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Potential therapeutics for SARS / transcription coactivator activity / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / nucleus / membrane
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / TATA box binding protein associated factor ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Bromodomain-like / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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: 2.3 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
DepositionDec 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 2.0Sep 13, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.entity_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 3.0Apr 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_entity_id ..._atom_site.auth_seq_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_asym.entity_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_seq_id
Revision 3.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
E: histone 4 peptide (H4K8acK12ac)
F: histone 4 peptide (H4K8acK12ac)


Theoretical massNumber of molelcules
Total (without water)62,6266
Polymers62,6266
Non-polymers00
Water2,234124
1
A: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
E: histone 4 peptide (H4K8acK12ac)


Theoretical massNumber of molelcules
Total (without water)31,3133
Polymers31,3133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-15 kcal/mol
Surface area14350 Å2
MethodPISA
2
B: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
F: histone 4 peptide (H4K8acK12ac)


Theoretical massNumber of molelcules
Total (without water)31,3133
Polymers31,3133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-17 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.600, 99.600, 136.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 15099.380 Da / Num. of mol.: 4 / Fragment: unp resideus 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 4 peptide (H4K8acK12ac) / peptide (H4K8acK12ac)


Mass: 1114.301 Da / Num. of mol.: 2 / Fragment: unp residues 8-18 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density meas: 54.56 Mg/m3 / Density % sol: 54.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, 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 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionRedundancy: 9 % / Av σ(I) over netI: 3.1 / Number: 281101 / Rsym value: 0.146 / D res high: 2.3 Å / D res low: 40.25 Å / Num. obs: 31295 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.2740.2598.910.090.098
5.147.2710010.0960.0968.5
4.25.1410010.1130.1138.5
3.644.210010.1240.1248.9
3.253.6410010.1270.1279.1
2.973.2510010.1770.1779.2
2.752.9710010.2630.2639.2
2.572.7510010.4190.4199.3
2.422.5710010.6290.6299.3
2.32.4210010.980.988.8
ReflectionResolution: 2.3→42.33 Å / Num. all: 31295 / Num. obs: 31295 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.428.80.980.83962645010.98100
2.42-2.579.30.6291.23922842200.629100
2.57-2.759.30.4191.83718740150.419100
2.75-2.979.20.2632.83453037420.263100
2.97-3.259.20.17743149234410.177100
3.25-3.649.10.12752852331500.127100
3.64-4.28.90.1244.82496028020.124100
4.2-5.148.50.1135.22043824010.113100
5.14-7.278.50.0965.81614419040.096100
7.27-40.2580.095.7897311190.0998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.76 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.25 Å
Translation2.5 Å40.25 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: 2.3→42.33 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2665 / WRfactor Rwork: 0.2087 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8227 / SU B: 13.84 / SU ML: 0.17 / SU R Cruickshank DPI: 0.2489 / SU Rfree: 0.2192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1575 5 %RANDOM
Rwork0.1998 ---
all0.2026 31256 --
obs0.2026 31231 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.17 Å2 / Biso mean: 53.129 Å2 / Biso min: 20.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 12 124 3928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023918
X-RAY DIFFRACTIONr_bond_other_d0.0030.022614
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.965337
X-RAY DIFFRACTIONr_angle_other_deg1.6883.0056365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37225.851188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70115647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.154157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 106 -
Rwork0.276 1947 -
all-2053 -
obs--99.9 %
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)
12.0901-0.4561-1.31995.35572.91515.3152-0.02440.03510.19160.1031-0.07950.15710.19260.00180.10380.0415-0.0255-0.01640.05050.04730.071534.494217.649752.9451
25.8511-2.1354-0.74037.3505-1.39313.35570.12720.23290.44490.04060.0414-0.145-0.3246-0.2198-0.16860.06390.06210.05370.10950.07520.075139.996326.896428.265
34.08811.07281.57155.51640.30215.6920.45230.0491-0.1826-0.0359-0.3350.38070.6826-0.1943-0.11730.32680.03520.00720.1335-0.12330.165722.3642-1.164327.5994
46.8787-0.432-0.38113.3838-0.06092.09010.1061-0.21040.12140.0359-0.12330.03490.0869-0.08620.01730.06550.0225-0.01650.1148-0.05890.09988.573922.343729.7943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 166
2X-RAY DIFFRACTION2B58 - 166
3X-RAY DIFFRACTION3C56 - 167
4X-RAY DIFFRACTION4D59 - 167

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