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- PDB-7b7g: BAZ2A bromodomain in complex with compounds MS04 and B11 -

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Basic information

Entry
Database: PDB / ID: 7b7g
TitleBAZ2A bromodomain in complex with compounds MS04 and B11
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of transcription by RNA polymerase I / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of transcription by RNA polymerase I / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-T1B / Chem-T1E / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.428 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Sedykh, M. / Caflisch, A. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
Citation
Journal: Acs Med.Chem.Lett. / Year: 2022
Title: Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing.
Authors: Dalle Vedove, A. / Cazzanelli, G. / Batiste, L. / Marchand, J.R. / Spiliotopoulos, D. / Corsi, J. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
#1: Journal: ACS Bio Med Chem Au / Year: 2021
Title: Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining
Authors: Dalle Vedove, A. / Cazzanelli, G. / Corsi, J. / Sedykh, M. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
History
DepositionDec 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8983
Polymers12,3641
Non-polymers5342
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6600 Å2
Unit cell
Length a, b, c (Å)37.424, 35.302, 37.802
Angle α, β, γ (deg.)90.000, 92.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / hWALp3


Mass: 12363.872 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 1796-1899) / Mutation: E1845H, L1848S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-T1B / 5-ethyl-2-(3-methyl-1,2,3-triazol-4-yl)-1~{H}-benzimidazole


Mass: 227.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-T1E / 1-[1-(3,5-dimethoxyphenyl)piperidin-4-yl]-2,3-dimethyl-guanidine


Mass: 306.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.02 Å3/Da / Density % sol: 39.03 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.428→37.761 Å / Num. obs: 18149 / % possible obs: 98.3 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.455.60.248268580.9770.0920.2216.695
7.82-37.765.80.067471280.9980.0250.06526.298.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mgj

5mgj


Resolution: 1.428→37.761 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1605 875 4.82 %
Rwork0.1341 17266 -
obs0.1354 18141 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.68 Å2 / Biso mean: 17.6849 Å2 / Biso min: 7.08 Å2
Refinement stepCycle: final / Resolution: 1.428→37.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 39 137 1042
Biso mean--26.41 26.35 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008992
X-RAY DIFFRACTIONf_angle_d0.9421351
X-RAY DIFFRACTIONf_chiral_restr0.067131
X-RAY DIFFRACTIONf_plane_restr0.005177
X-RAY DIFFRACTIONf_dihedral_angle_d28.382379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4283-1.51770.16821900.1077275796
1.5177-1.63490.16261560.1079281298
1.6349-1.79950.1439860.1178290998
1.7995-2.05980.16781590.1233286799
2.0598-2.59510.15921450.1364292499
2.5951-37.7610.15931390.14922997100

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