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- PDB-4xy8: Crystal Structure of the bromodomain of BRD9 in complex with a 2-... -

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Basic information

Entry
Database: PDB / ID: 4xy8
TitleCrystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / Bromodomain / ligand / complex / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
6-(5-bromo-2-methoxyphenyl)-9H-purin-2-amine / BROMIDE ION / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPicaud, S. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Filippakopoulos, P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust095751/Z/11/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2015
Title: 9H-Purine Scaffold Reveals Induced-Fit Pocket Plasticity of the BRD9 Bromodomain.
Authors: Picaud, S. / Strocchia, M. / Terracciano, S. / Lauro, G. / Mendez, J. / Daniels, D.L. / Riccio, R. / Bifulco, G. / Bruno, I. / Filippakopoulos, P.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6503
Polymers14,2501
Non-polymers4002
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-1 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.716, 43.604, 40.880
Angle α, β, γ (deg.)90.000, 104.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-487-

HOH

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Components

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


Mass: 14249.763 Da / Num. of mol.: 1 / Fragment: UNP residues 14-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Details (production host): pNIC28-Bsa4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q9H8M2
#2: Chemical ChemComp-43U / 6-(5-bromo-2-methoxyphenyl)-9H-purin-2-amine


Mass: 320.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10BrN5O
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M NaBr, 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionResolution: 1.7→19.559 Å / Num. all: 14841 / Num. obs: 14841 / % possible obs: 97.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.029 / Rrim(I) all: 0.09 / Rsym value: 0.086 / Net I/av σ(I): 7.4 / Net I/σ(I): 20.3 / Num. measured all: 142203
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.799.40.3377.41935220640.1150.3377.495.2
1.79-1.99.60.242.91927120040.0810.2410.196.1
1.9-2.039.60.1674.11843219130.0560.16713.697
2.03-2.199.70.11661738317940.0390.11618.597.9
2.19-2.49.70.0967.21619816740.0320.09622.298.4
2.4-2.699.70.0877.71447614970.0290.08725.298.8
2.69-3.19.70.0768.71303813440.0260.07629.199.5
3.1-3.89.60.05710.91098911470.0190.05735.199.8
3.8-5.389.50.05311.885159010.0180.05338100
5.38-19.55990.06945495030.020.0635.398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.55 Å
Translation3.5 Å19.55 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.21data scaling
PHASER2.1.4phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.7→19.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1883 / WRfactor Rwork: 0.1458 / FOM work R set: 0.9032 / SU B: 2.657 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0898 / SU Rfree: 0.0924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 748 5 %RANDOM
Rwork0.1482 14086 --
obs0.1502 14086 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.61 Å2 / Biso mean: 15.873 Å2 / Biso min: 3.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.57 Å2
2--0.03 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.7→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 20 191 1131
Biso mean--6.78 27.17 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019978
X-RAY DIFFRACTIONr_bond_other_d0.0010.02961
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9991316
X-RAY DIFFRACTIONr_angle_other_deg0.8283.0042217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5595116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08222.92741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.703156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_mcbond_it2.5571.57455
X-RAY DIFFRACTIONr_mcbond_other2.5581.549454
X-RAY DIFFRACTIONr_mcangle_it3.362.893568
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 43 -
Rwork0.174 972 -
all-1015 -
obs--92.44 %
Refinement TLS params.Method: refined / Origin x: 25.9548 Å / Origin y: 15.74 Å / Origin z: -10.722 Å
111213212223313233
T0.0188 Å20.0031 Å20.0088 Å2-0.0181 Å2-0.0015 Å2--0.0176 Å2
L0.7364 °2-0.4185 °20.5184 °2-0.3688 °2-0.2422 °2--0.3888 °2
S0.0074 Å °-0.02 Å °-0.0088 Å °0.0031 Å °0.011 Å °-0.0021 Å °0.0066 Å °-0.0131 Å °-0.0184 Å °

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