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- PDB-4yyj: Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide -

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Basic information

Entry
Database: PDB / ID: 4yyj
TitleCrystal structure of BRD9 Bromodomain bound to a butyryllysine peptide
Components
  • Bromodomain-containing protein 9
  • Histone H4
KeywordsPROTEIN BINDING / Bromodomain-butyryllysine 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 ...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 / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nucleic acid binding / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone H4, conserved site / Histone H4 signature. / Histone H4 ...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 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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 / molecular replacement / Resolution: 1.85 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)52,0066
Polymers52,0066
Non-polymers00
Water2,522140
1
A: Bromodomain-containing protein 9
B: Bromodomain-containing protein 9
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)26,0033
Polymers26,0033
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)26,0033
Polymers26,0033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.823, 34.331, 129.067
Angle α, β, γ (deg.)90.860, 90.000, 111.190
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: 1114.279 Da / Num. of mol.: 2 / Fragment: N-terminal tail (UNP residues 2-12) / Source method: obtained synthetically / Details: lysine residues butyrylated / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 32888 / % possible obs: 97.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.077 / Χ2: 1.034 / Net I/av σ(I): 9.343 / Net I/σ(I): 7.8 / Num. measured all: 64982
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.921.90.3733131.11195.9
1.92-1.9920.25432051.00596.8
1.99-2.0820.18432731.00596.6
2.08-2.1920.14132981.04697.1
2.19-2.3320.11932711.00697.3
2.33-2.5120.09932891.00597.9
2.51-2.7620.08533381.0398.2
2.76-3.1620.07733031.06998.2
3.16-3.9920.06232781.03397.8
3.99-5020.05533201.0397.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HME

3hme


Resolution: 1.85→32.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.922 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1659 5 %RANDOM
Rwork0.1984 ---
obs0.2008 31200 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 310.37 Å2 / Biso mean: 27.473 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.02 Å2-0.05 Å2
2--0.02 Å2-0.03 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.85→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 140 3512
Biso mean---25.98 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193458
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9724634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69223.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.515624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7631512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212568
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 116 -
Rwork0.228 2304 -
all-2420 -
obs--93.22 %
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)
12.1664-0.4918-0.94122.16321.29083.3713-0.0125-0.0465-0.02820.06950.00980.0242-0.0443-0.01160.00270.0554-0.0101-0.01510.0373-0.01060.013-57.001229.32581.7788
22.2430.64630.95182.20841.28163.3077-0.0110.06910.036-0.06060.01260.03480.0512-0.0064-0.00160.04130.0167-0.0090.0272-0.00610.0036-57.00436.1726-30.5317
31.8369-0.70451.32142.172-1.68553.7575-0.01080.00410.09330.02580.0066-0.03530.05570.01010.00420.0484-0.0086-0.00490.03690.00940.0091-63.21435.181666.2951
42.05080.5383-1.39621.9752-1.69073.6053-0.0134-0.0028-0.1117-0.0255-0.0149-0.0526-0.07130.02630.02840.06520.0041-0.01250.03730.00490.0149-63.227628.219233.9993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 122
2X-RAY DIFFRACTION2B22 - 122
3X-RAY DIFFRACTION3C4 - 9
4X-RAY DIFFRACTION4D22 - 122

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