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- PDB-4yyi: Crystal structure of BRD9 Bromodomain bound to an acetylated peptide -

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Basic information

Entry
Database: PDB / ID: 4yyi
TitleCrystal structure of BRD9 Bromodomain bound to an acetylated peptide
Components
  • Bromodomain-containing protein 9
  • Histone H4
KeywordsPROTEIN BINDING / Bromodomain-acetyllysine complex
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / 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 ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / 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 / telomere organization / Meiotic synapsis / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lysine-acetylated histone binding / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nucleic acid binding / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTang, Y. / Bellon, S. / Cochran, A.G. / Poy, F.
CitationJournal: Structure / Year: 2015
Title: A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications.
Authors: Flynn, E.M. / Huang, O.W. / Poy, F. / Oppikofer, M. / Bellon, S.F. / Tang, Y. / Cochran, A.G.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Sep 27, 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
B: Bromodomain-containing protein 9
C: Histone H4
D: Bromodomain-containing protein 9
E: Bromodomain-containing protein 9
F: Histone H4


Theoretical massNumber of molelcules
Total (without water)51,8946
Polymers51,8946
Non-polymers00
Water5,170287
1
A: Bromodomain-containing protein 9
B: Bromodomain-containing protein 9
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)25,9473
Polymers25,9473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Bromodomain-containing protein 9
E: Bromodomain-containing protein 9
F: Histone H4


Theoretical massNumber of molelcules
Total (without water)25,9473
Polymers25,9473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.746, 34.602, 129.361
Angle α, β, γ (deg.)88.790, 90.000, 68.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8 / BRD9


Mass: 12444.461 Da / Num. of mol.: 4 / Fragment: bromodomain (UNP residues 17-123)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H8M2
#2: Protein/peptide Histone H4


Mass: 1058.173 Da / Num. of mol.: 2 / Fragment: N-terminal tail (UNP residues 2-12) / Source method: obtained synthetically / Details: lysine residues acetylated / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.556
11H, H-K, -L20.444
ReflectionResolution: 1.5→50 Å / Num. obs: 60687 / % possible obs: 95.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.05 / Χ2: 1.033 / Net I/av σ(I): 15.339 / Net I/σ(I): 11.1 / Num. measured all: 138541
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.552.30.30460451.01194
1.55-1.622.30.23859851.02594.7
1.62-1.692.30.17860601.04794.8
1.69-1.782.30.14161061.0495.3
1.78-1.892.30.1160731.02494.6
1.89-2.042.30.08760501.0395
2.04-2.242.30.06760531.0195.1
2.24-2.562.30.0660681.03495.6
2.56-3.232.30.04862041.04297.2
3.23-502.20.04160431.06594.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HME

3hme


Resolution: 1.5→32.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.646 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 3019 5 %RANDOM
Rwork0.206 ---
obs0.2077 57639 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.67 Å2 / Biso mean: 26.997 Å2 / Biso min: 14.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20.83 Å2-0.43 Å2
2---2.79 Å2-0.45 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.5→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 287 3639
Biso mean---31.02 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0193438
X-RAY DIFFRACTIONr_angle_refined_deg2.7521.974610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75123.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34515622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81512
X-RAY DIFFRACTIONr_chiral_restr0.1930.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212560
X-RAY DIFFRACTIONr_mcbond_it2.5161.8871650
X-RAY DIFFRACTIONr_mcangle_it3.1022.8282052
X-RAY DIFFRACTIONr_scbond_it3.1592.0931788
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 225 -
Rwork0.217 3897 -
all-4122 -
obs--86.52 %
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)
11.4978-0.24360.55261.229-0.57521.2405-0.02920.09110.03530.04030.0065-0.00420.0515-0.01530.02270.0675-0.02330.00520.03210.0130.010455.7295-31.70132.0209
21.48880.1608-0.67981.1521-0.62731.5659-0.0363-0.0816-0.0547-0.04380.0018-0.0013-0.0599-0.00490.03450.0645-0.00220.00680.04450.01920.011255.7681-8.8948-30.0271
31.39620.09350.66360.98460.6711.4123-0.0222-0.09790.0456-0.0186-0.00150.01010.06060.00560.02370.0716-0.01110.00710.0274-0.01380.008261.898-30.348134.5486
41.4765-0.1311-0.52551.1370.62171.31-0.02060.0819-0.04610.01870.00040.0073-0.0463-0.00620.02020.0684-0.01950.00780.019-0.00870.004261.9143-7.24866.7665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 122
2X-RAY DIFFRACTION2B23 - 122
3X-RAY DIFFRACTION3D22 - 122
4X-RAY DIFFRACTION4E22 - 122

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