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- PDB-4yyh: Crystal structure of BRD9 Bromodomain bound to a crotonyllysine p... -

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Basic information

Entry
Database: PDB / ID: 4yyh
TitleCrystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide
Components
  • Bromodomain-containing protein 9
  • Histone H4
KeywordsPROTEIN BINDING / Bromodomain-crotonyllysine 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 / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / 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 / 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 / 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 / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / 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 H4, conserved site / Histone H4 signature. / Histone H4 / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone Acetyltransferase; Chain A / 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: 1.74 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_1 / _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 9
B: Bromodomain-containing protein 9
Z: Histone H4
Y: Histone H4


Theoretical massNumber of molelcules
Total (without water)27,1094
Polymers27,1094
Non-polymers00
Water3,639202
1
A: Bromodomain-containing protein 9
Z: Histone H4


Theoretical massNumber of molelcules
Total (without water)13,5552
Polymers13,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
Y: Histone H4


Theoretical massNumber of molelcules
Total (without water)13,5552
Polymers13,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.147, 35.700, 65.019
Angle α, β, γ (deg.)90.000, 99.010, 90.000
Int Tables number5
Space group name H-MC121

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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.: 2 / 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: 1110.249 Da / Num. of mol.: 2 / Fragment: N-terminal tail (UNP residues 2-12) / Source method: obtained synthetically / Details: lysine residues crotonylated / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate, pH 5.5, 0.2 M sodium 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: 1.74→50 Å / Num. obs: 29841 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Χ2: 1.036 / Net I/av σ(I): 20.996 / Net I/σ(I): 11.8 / Num. measured all: 108728
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.74-1.83.70.57329381.013100
1.8-1.873.70.37829831.082100
1.87-1.963.70.26429361.092100
1.96-2.063.70.17129781.046100
2.06-2.193.70.11429801.012100
2.19-2.363.70.0929731.055100
2.36-2.63.70.07429991100
2.6-2.983.60.06129901.00199.8
2.98-3.753.50.04229821.01199.5
3.75-503.60.03530821.04798.7

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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: 1.74→29.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.675 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1511 5.1 %RANDOM
Rwork0.2119 ---
obs0.2142 28245 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.46 Å2 / Biso mean: 33.753 Å2 / Biso min: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å20.06 Å2
2---0.02 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.74→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 0 202 1925
Biso mean---39.07 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191765
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.9762362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9955209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85623.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.863156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211320
LS refinement shellResolution: 1.737→1.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 124 -
Rwork0.335 1978 -
all-2102 -
obs--97 %
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)
13.3204-0.27270.09930.7450.02970.87480.0688-0.114-0.01770.0607-0.0519-0.0381-0.04730.1562-0.01690.0631-0.0235-0.02540.04970.00450.012-17.2787-11.71752.0179
23.2305-0.89830.08041.14140.02650.83620.0362-0.07560.11360.0573-0.0092-0.0196-0.01350.124-0.0270.0619-0.0144-0.02120.0388-0.00660.016-22.1494-4.310334.0474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 123
2X-RAY DIFFRACTION2B21 - 123

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