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- PDB-3muk: Crystal structure of Brd4 bromodomain 1 with propionylated histon... -

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Basic information

Entry
Database: PDB / ID: 3muk
TitleCrystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23
Components
  • Bromodomain-containing protein 4BRD4
  • peptide of Histone H3.3
KeywordsSIGNALING PROTEIN / bromodomain / histone recognition / N-propionyl lysine / acylation
Function / homology
Function and homology information


GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / positive regulation of T-helper 17 cell lineage commitment / nucleosomal DNA binding / inner cell mass cell proliferation / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding ...GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / positive regulation of T-helper 17 cell lineage commitment / nucleosomal DNA binding / inner cell mass cell proliferation / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Inhibition of DNA recombination at telomere / positive regulation of G2/M transition of mitotic cell cycle / telomere organization / histone reader activity / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / RNA polymerase II CTD heptapeptide repeat kinase activity / DNA methylation / Condensation of Prophase Chromosomes / 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 / chromosome segregation / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / transcription coregulator activity / 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 / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / chromosome / 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 / positive regulation of canonical NF-kappaB signal transduction / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / 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 / 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. / Histone H3 signature 2. ...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. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain-like / Histone Acetyltransferase; Chain 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: 1.75 Å
AuthorsVollmuth, F. / Geyer, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains
Authors: Vollmuth, F. / Geyer, M.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
D: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3383
Polymers16,2762
Non-polymers621
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.213, 47.008, 78.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Mitotic chromosome-associated protein / MCAP


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


Mass: 890.040 Da / Num. of mol.: 1 / Fragment: histone H3 peptide, UNP residues 22-29 / Source method: obtained synthetically / Details: Fmoc solid phase synthesis / References: UniProt: P84243
#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.: 151 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, 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: Nov 15, 2009
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→19.6 Å / Num. all: 13605 / Num. obs: 13605 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.1
Reflection shellResolution: 1.75→1.8 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1072 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JVJ

3jvj


Resolution: 1.75→19.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.057 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21879 730 5.4 %RANDOM
Rwork0.17206 ---
obs0.17451 12865 99.76 %-
all-12865 --
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: 29.685 Å2
Baniso -1Baniso -2Baniso -3
1-4.84 Å20 Å20 Å2
2---2.41 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 4 151 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221109
X-RAY DIFFRACTIONr_bond_other_d0.0010.02734
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9711516
X-RAY DIFFRACTIONr_angle_other_deg1.05131814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43325.91849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.363152
X-RAY DIFFRACTIONr_chiral_restr0.1160.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02200
X-RAY DIFFRACTIONr_nbd_refined0.2320.2257
X-RAY DIFFRACTIONr_nbd_other0.1840.2702
X-RAY DIFFRACTIONr_nbtor_refined0.20.2551
X-RAY DIFFRACTIONr_nbtor_other0.1020.2493
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3160.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.227
X-RAY DIFFRACTIONr_mcbond_it1.2261.5713
X-RAY DIFFRACTIONr_mcbond_other0.3751.5259
X-RAY DIFFRACTIONr_mcangle_it1.7921112
X-RAY DIFFRACTIONr_scbond_it2.7813475
X-RAY DIFFRACTIONr_scangle_it3.74.5402
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 44 -
Rwork0.233 938 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -5.9577 Å / Origin y: 2.0343 Å / Origin z: 7.6689 Å
111213212223313233
T-0.0842 Å20.0053 Å2-0.0324 Å2--0.0027 Å20.0098 Å2---0.0129 Å2
L0.6217 °2-0.1303 °20.2882 °2-2.4222 °21.15 °2--1.6783 °2
S-0.0427 Å °0.0013 Å °0.0214 Å °-0.2167 Å °-0.063 Å °0.1291 Å °-0.3039 Å °-0.1262 Å °0.1057 Å °

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