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- PDB-3jvk: Crystal structure of bromodomain 1 of mouse Brd4 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3jvk
TitleCrystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14
Components
  • Bromodomain-containing protein 4
  • histone H3.3 peptide
KeywordsSIGNALING PROTEIN / bromodomain / alpha helical / N-acetyl lysine recognition
Function / homology
Function and homology information


GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / inner cell mass cell proliferation ...GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / inner cell mass cell proliferation / nucleus organization / RNA polymerase II C-terminal domain binding / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of T-helper 17 cell lineage commitment / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / positive regulation of G2/M transition of mitotic cell cycle / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / RNA polymerase II CTD heptapeptide repeat kinase activity / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / condensed nuclear chromosome / Defective pyroptosis / chromosome segregation / RNA Polymerase I Promoter Escape / positive regulation of transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / p53 binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / positive regulation of canonical NF-kappaB signal transduction / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / 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 H3 signature 1. / Bromodomain-like ...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 H3 signature 1. / Bromodomain-like / Histone H3 signature 2. / Histone Acetyltransferase; Chain A / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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
Histone H3.3 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVollmuth, F. / Blankenfeldt, W. / Geyer, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structures of the Dual Bromodomains of the P-TEFb-activating Protein Brd4 at Atomic Resolution
Authors: Vollmuth, F. / Blankenfeldt, W. / Geyer, M.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Nov 22, 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
C: histone H3.3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3333
Polymers16,2712
Non-polymers621
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-1 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.131, 47.030, 77.250
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 / Mitotic chromosome-associated protein / MCAP


Mass: 15385.665 Da / Num. of mol.: 1 / Fragment: bromodomain 1, UNP residues 42-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brd4 / Plasmid: pProEx-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ESU6
#2: Protein/peptide histone H3.3 peptide


Mass: 885.023 Da / Num. of mol.: 1 / Fragment: UNP residues 13-20 / Source method: obtained synthetically / Details: Fmoc solid phase synthesis / References: UniProt: P84243
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.6M Na formate, 10% glycerol, soaked with 10-times excess of histone peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2009
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.71 Å / Num. all: 12652 / Num. obs: 12652 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.367 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.53
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 4.7 / Num. measured obs: 14698 / Num. unique obs: 1857 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OSS

2oss


Resolution: 1.8→19.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.372 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 685 5.4 %RANDOM
Rwork0.196 ---
all0.196 12646 --
obs0.2 12646 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.489 Å2
Baniso -1Baniso -2Baniso -3
1-7.22 Å20 Å20 Å2
2---3.78 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 4 104 1199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221130
X-RAY DIFFRACTIONr_bond_other_d0.0010.02761
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9811548
X-RAY DIFFRACTIONr_angle_other_deg1.08831883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17725.68651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93115188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.132153
X-RAY DIFFRACTIONr_chiral_restr0.1090.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined0.2360.2261
X-RAY DIFFRACTIONr_nbd_other0.1950.2773
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2552
X-RAY DIFFRACTIONr_nbtor_other0.0960.2550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.26
X-RAY DIFFRACTIONr_mcbond_it1.781.5715
X-RAY DIFFRACTIONr_mcbond_other0.7321.5261
X-RAY DIFFRACTIONr_mcangle_it2.51721119
X-RAY DIFFRACTIONr_scbond_it3.7523497
X-RAY DIFFRACTIONr_scangle_it4.9834.5423
X-RAY DIFFRACTIONr_rigid_bond_restr2.01332157
X-RAY DIFFRACTIONr_sphericity_free14.1573104
X-RAY DIFFRACTIONr_sphericity_bonded4.831857
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 51 -
Rwork0.291 844 -
all-895 -
obs--99.89 %

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