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- PDB-8sb6: Structure of human BRD2-BD1 bound to a histone H4 acetyl-methylly... -

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Basic information

Entry
Database: PDB / ID: 8sb6
TitleStructure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide
Components
  • Bromodomain containing 2
  • Histone H4
KeywordsPEPTIDE BINDING PROTEIN / histone peptide protein complex
Function / homology
Function and homology information


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 ...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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / 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 / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear speck / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / RNA 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 ...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 / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 2 / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsConnor, L.J. / Ekundayo, B.E. / Lu-Culligan, W.J. / Simon, M.D. / Bleichert, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141313 United States
CitationJournal: Nature / Year: 2023
Title: Acetyl-methyllysine marks chromatin at active transcription start sites.
Authors: Lu-Culligan, W.J. / Connor, L.J. / Xie, Y. / Ekundayo, B.E. / Rose, B.T. / Machyna, M. / Pintado-Urbanc, A.P. / Zimmer, J.T. / Vock, I.W. / Bhanu, N.V. / King, M.C. / Garcia, B.A. / Bleichert, F. / Simon, M.D.
History
DepositionApr 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain containing 2
B: Bromodomain containing 2
C: Bromodomain containing 2
D: Histone H4
E: Histone H4


Theoretical massNumber of molelcules
Total (without water)46,8625
Polymers46,8625
Non-polymers00
Water3,855214
1
A: Bromodomain containing 2
D: Histone H4


Theoretical massNumber of molelcules
Total (without water)16,0882
Polymers16,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain containing 2
E: Histone H4


Theoretical massNumber of molelcules
Total (without water)16,0882
Polymers16,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain containing 2


Theoretical massNumber of molelcules
Total (without water)14,6871
Polymers14,6871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.378, 55.819, 68.006
Angle α, β, γ (deg.)90.000, 94.414, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-241-

HOH

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Components

#1: Protein Bromodomain containing 2 / Bromodomain-containing protein 2


Mass: 14687.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: H0Y6K2
#2: Protein/peptide Histone H4 /


Mass: 1400.588 Da / Num. of mol.: 2 / Fragment: N-terminal peptide (UNP residues 2-16) / 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.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→67.8 Å / Num. obs: 41240 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 2265 / CC1/2: 0.338

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ONY

6ony


Resolution: 1.8→67.8 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8188
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2041 1930 4.84 %
Rwork0.1806 37941 -
obs0.1818 39871 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 34 214 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01512851
X-RAY DIFFRACTIONf_angle_d1.17393851
X-RAY DIFFRACTIONf_chiral_restr0.0758404
X-RAY DIFFRACTIONf_plane_restr0.0109484
X-RAY DIFFRACTIONf_dihedral_angle_d15.55911072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.36161580.3222690X-RAY DIFFRACTION99.68
1.85-1.890.30311240.28422704X-RAY DIFFRACTION99.4
1.89-1.950.29281310.24962712X-RAY DIFFRACTION99.41
1.95-2.010.26411420.23422707X-RAY DIFFRACTION99.75
2.01-2.090.24781330.21412676X-RAY DIFFRACTION99.29
2.09-2.170.22331480.17752678X-RAY DIFFRACTION99.75
2.17-2.270.18031210.17522733X-RAY DIFFRACTION98.93
2.27-2.390.22961380.16962687X-RAY DIFFRACTION99.16
2.39-2.540.19661390.16852707X-RAY DIFFRACTION98.72
2.54-2.730.22051360.18122695X-RAY DIFFRACTION99.44
2.73-3.010.19891370.17382718X-RAY DIFFRACTION99.51
3.01-3.440.20531420.17712727X-RAY DIFFRACTION99.34
3.44-4.340.15311410.15012723X-RAY DIFFRACTION98.86
4.34-67.80.19541400.1742784X-RAY DIFFRACTION98.38
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)
11.840131553360.4318294517910.04333048940361.9505838849-0.06550894132171.74002803123-0.008576754128990.0748455240783-0.0224091309387-0.1260968759490.00268347174236-0.162904764590.04861621338470.178266044396-0.00119670814940.1587263071750.001572502159930.0230192550610.1780971270590.0007395435468050.202301284329-19.49744403160.67797233023432.4183573561
21.27707998260.2825790945270.09269340778081.976808154710.1070476697462.096308879370.03255435419720.1218078136190.0468412087118-0.244253471584-0.006018091736010.0986785808855-0.028235087406-0.0257202188564-3.04462698713E-80.2128618441890.00287015761576-0.02816095872110.1717729359920.004538360816970.211988806052-37.66701100032.208133708623.4608814432
31.65232413063-0.1950476892571.201583861441.459594775210.01388526373874.990119063410.0587865679565-0.0692585958886-0.005373854736050.1266782823650.1312266157240.04282218074380.0384118912954-0.2449187363580.0008017565197980.1941842642170.004335816253310.0009182959686230.3011157575330.001295653886290.196111044967-0.78209954535612.623676915110.2382138416
40.02636403866530.005530461927330.0079232304520.001179325543270.000577328550460.0183150132097-0.333085187477-0.6925190867360.4264691016640.695400991529-0.1711969246340.1951912533270.257896710909-0.7187344848153.90251881117E-50.539502392160.002222467983750.024097518860.516954857682-0.1061816213970.445475852285-29.1101734082.5210900105347.914442919
50.01948374784970.0115219115706-0.005489863878590.01282942716070.009900925183640.0299825712510.638567085422-0.9227433121920.0800185773830.356996619751-0.1952371988030.891400889058-0.152896557697-0.1225658609316.1071955696E-60.429771542296-0.1233222119950.05592906503610.562850540034-0.02149529724010.653385177555-44.35446382530.076400366740339.7497895465
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 76 through 183)AA76 - 1831 - 108
22(chain 'B' and resid 76 through 182)BB76 - 1821 - 107
33(chain 'C' and resid 76 through 181)CC76 - 1811 - 106
44(chain 'D' and resid 1 through 6)DD - F1 - 61 - 6
55(chain 'E' and resid 1 through 6)EG - I1 - 61 - 6

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