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

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Basic information

Entry
Database: PDB / ID: 3uvy
TitleCrystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac)
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 / 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: 2.02 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
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
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


Theoretical massNumber of molelcules
Total (without water)16,5802
Polymers16,5802
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.225, 50.478, 51.969
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 / 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 (H4K16acK20ac)


Mass: 1480.718 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 16-26 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.71 Å3/Da / Density meas: 28.06 Mg/m3 / Density % sol: 28.06 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 5.4 / Number: 33296 / Rsym value: 0.135 / D res high: 2.02 Å / D res low: 43.225 Å / Num. obs: 7866 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.3943.2296.210.0420.0423.5
4.526.3999.610.0550.0553.9
3.694.5299.410.0580.0584
3.193.6999.710.0790.0794.2
2.863.1999.710.1310.1314.3
2.612.8610010.1870.1874.3
2.412.6199.910.2690.2694.3
2.262.4199.910.3760.3764.3
2.132.2699.910.4750.4754.4
2.022.1310010.8310.8314.4
ReflectionResolution: 2.02→43.225 Å / Num. all: 7890 / Num. obs: 7866 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.02-2.134.40.8310.9487111180.831100
2.13-2.264.40.4751.6463610640.47599.9
2.26-2.414.30.3762.1437810110.37699.9
2.41-2.614.30.2692.840149290.26999.9
2.61-2.864.30.1874.137188630.187100
2.86-3.194.30.1315.833807940.13199.7
3.19-3.694.20.0799.529537080.07999.7
3.69-4.5240.05812.124446060.05899.4
4.52-6.393.90.05511.818724810.05599.6
6.39-43.2253.50.04214.210302920.04296.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.55 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.98 Å
Translation2.5 Å25.98 Å

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Processing

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

2oss

2ouo

2grc

2oo1

3dai

3d7c


Resolution: 2.02→43.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2356 / WRfactor Rwork: 0.1635 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7834 / SU B: 11.726 / SU ML: 0.172 / SU R Cruickshank DPI: 0.2215 / SU Rfree: 0.2036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 459 5.9 %RANDOM
Rwork0.1811 ---
all0.1856 7857 --
obs0.1856 7828 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.14 Å2 / Biso mean: 28.0894 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2---1.92 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.02→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 65 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221037
X-RAY DIFFRACTIONr_bond_other_d0.0020.02711
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9671396
X-RAY DIFFRACTIONr_angle_other_deg1.00931734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37124.90653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71915179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.687155
X-RAY DIFFRACTIONr_chiral_restr0.0810.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02207
X-RAY DIFFRACTIONr_mcbond_it4.0343603
X-RAY DIFFRACTIONr_mcbond_other1.2643242
X-RAY DIFFRACTIONr_mcangle_it5.8575970
X-RAY DIFFRACTIONr_scbond_it9.158434
X-RAY DIFFRACTIONr_scangle_it11.27311424
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 22 -
Rwork0.354 544 -
all-566 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: 59.6893 Å / Origin y: 22.9907 Å / Origin z: 10.0539 Å
111213212223313233
T0.1183 Å2-0.009 Å20.0035 Å2-0.0186 Å20.0047 Å2--0.0181 Å2
L1.0619 °20.3348 °20.6206 °2-0.474 °20.2398 °2--0.4984 °2
S-0.0082 Å °-0.0163 Å °-0.0347 Å °-0.0671 Å °-0.0009 Å °-0.0532 Å °-0.0032 Å °-0.0483 Å °0.0091 Å °

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