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- PDB-5hjc: BRD3 second bromodomain in complex with histone H3 acetylation at K18 -

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Basic information

Entry
Database: PDB / ID: 5hjc
TitleBRD3 second bromodomain in complex with histone H3 acetylation at K18
Components
  • Bromodomain-containing protein 3
  • peptide of Histone H3.1
KeywordsSIGNALING PROTEIN/PEPTIDE / Complex / BRD3 / Bromodomain / histone peptide / acetyllysine / H3K18 / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / protein localization to chromatin / telomere organization / molecular condensate scaffold activity / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...lncRNA binding / endodermal cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / protein localization to chromatin / telomere organization / molecular condensate scaffold activity / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / 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 / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / 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 / HDMs demethylate histones / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
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 ...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 H3.1 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, Y.Y. / Zhao, D. / Guan, H.P. / Li, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China91519304 China
CitationJournal: Mol.Cell / Year: 2016
Title: Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain
Authors: Li, Y.Y. / Sabari, B.R. / Panchenko, T. / Wen, H. / Zhao, D. / Guan, H.P. / Wan, L. / Huang, H. / Tang, Z. / Zhao, Y. / Roeder, R.G. / Shi, X. / Allis, C.D. / Li, H.T.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 15, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: peptide of Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1864
Polymers14,0882
Non-polymers982
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-8 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.768, 79.768, 95.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Bromodomain-containing protein 3 / / RING3-like protein


Mass: 13032.073 Da / Num. of mol.: 1 / Fragment: second bromodomain, UNP residues 307-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15059
#2: Protein/peptide peptide of Histone H3.1


Mass: 1056.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30%(w/v) polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 M MES, 0.1 M guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 5939 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.186 / Net I/av σ(I): 16.805 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.647.10.7961100
2.64-2.696.90.7561100
2.69-2.7470.6311100
2.74-2.870.4761100
2.8-2.8670.4691100
2.86-2.9370.4071100
2.93-36.90.3471100
3-3.086.90.291100
3.08-3.176.90.2751100
3.17-3.286.90.2151100
3.28-3.396.80.2071100
3.39-3.536.80.1661100
3.53-3.696.60.151100
3.69-3.886.70.1451100
3.88-4.136.50.1451100
4.13-4.456.40.1351100
4.45-4.896.50.126199.7
4.89-5.66.20.119199.4
5.6-7.056.40.119198.8
7.05-505.80.106194.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OO1

2oo1


Resolution: 2.6→28.852 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2691 291 4.91 %
Rwork0.2171 --
obs0.2195 5923 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.14 Å2 / Biso mean: 31.2308 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 2.6→28.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 5 52 1043
Biso mean--41.24 29.59 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021015
X-RAY DIFFRACTIONf_angle_d0.6371363
X-RAY DIFFRACTIONf_chiral_restr0.027138
X-RAY DIFFRACTIONf_plane_restr0.004176
X-RAY DIFFRACTIONf_dihedral_angle_d13.01393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5974-3.27170.33651480.252927342882
3.2717-28.85370.23371430.200828983041

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