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- PDB-6y7j: Structure of the BRD9 bromodomain and compound 15 -

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Basic information

Entry
Database: PDB / ID: 6y7j
TitleStructure of the BRD9 bromodomain and compound 15
ComponentsBromodomain-containing protein 9
KeywordsSTRUCTURAL GENOMICS / BRD9 / Bromodomain-containing protein 9
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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-OF5 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsDiaz-Saez, L. / Krojer, T. / Picaud, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative
CitationJournal: To Be Published
Title: Structure of the BRD9 bromodomain
Authors: Diaz-Saez, L. / Krojer, T. / Picaud, S. / von Delft, F. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M.
History
DepositionMar 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7506
Polymers28,0632
Non-polymers6874
Water4,846269
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3282
Polymers14,0311
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4224
Polymers14,0311
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.110, 118.690, 28.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A10 - 120
2010B10 - 120

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Components

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


Mass: 14031.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R2 / References: UniProt: Q9H8M2
#2: Chemical ChemComp-OF5 / 1-[8-(2,5-dimethoxyphenyl)pyrrolo[1,2-a]pyrimidin-6-yl]ethanone


Mass: 296.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium acetate, 25% PEG3350, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.6→62.86 Å / Num. obs: 34080 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.033 / Rrim(I) all: 0.081 / Net I/σ(I): 12 / Num. measured all: 202571 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.630.586925816700.4350.2740.6492.6100
8.76-62.860.0214882720.9990.010.02350.999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.36 Å62.86 Å
Translation4.36 Å62.86 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQ1

5mq1


Resolution: 1.6→62.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.466 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1686 5 %RANDOM
Rwork0.1933 ---
obs0.1959 32338 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92 Å2 / Biso mean: 28.47 Å2 / Biso min: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.6→62.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 49 269 2138
Biso mean--17.47 32.95 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191962
X-RAY DIFFRACTIONr_bond_other_d0.0020.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.9562.0022648
X-RAY DIFFRACTIONr_angle_other_deg1.0693.0054435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5915235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89223.41879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39215371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.267159
X-RAY DIFFRACTIONr_chiral_restr0.1210.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
Refine LS restraints NCS

Ens-ID: 1 / Number: 6802 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 117 -
Rwork0.325 2358 -
all-2475 -
obs--99.96 %

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