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- PDB-7b7b: BAZ2A bromodomain in complex with triazole compound MS04 -

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Basic information

Entry
Database: PDB / ID: 7b7b
TitleBAZ2A bromodomain in complex with triazole compound MS04
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 / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / 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 / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / 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 / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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)12,5912
Polymers12,3641
Non-polymers2271
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.119, 35.163, 37.525
Angle α, β, γ (deg.)90.000, 92.480, 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
Details: First two residues SM derive from the expression tag.
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.98 Å3/Da / Density % sol: 37.84 % / Mosaicity: 0.52 °
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: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→37.49 Å / Num. obs: 18984 / % possible obs: 98.7 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.026 / Rrim(I) all: 0.056 / Net I/σ(I): 16.8 / Num. measured all: 81556
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
1.4-1.424.30.83841739660.8050.4520.9561.997.8
7.54-37.493.70.0374941320.9980.020.04328.696.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5mgj


Resolution: 1.4→37.49 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 1072 5.65 %
Rwork0.1438 17898 -
obs0.1458 18970 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.87 Å2 / Biso mean: 16.7395 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: final / Resolution: 1.4→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 17 156 1039
Biso mean--13.82 26.25 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007965
X-RAY DIFFRACTIONf_angle_d0.8811313
X-RAY DIFFRACTIONf_chiral_restr0.068129
X-RAY DIFFRACTIONf_plane_restr0.006174
X-RAY DIFFRACTIONf_dihedral_angle_d27.015369
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.46370.36451300.3431220197
1.4637-1.54090.21151680.1704213697
1.5409-1.63740.21271430.1471220599
1.6374-1.76390.16651410.1233222599
1.7639-1.94140.19171310.1241224999
1.9414-2.22220.16421610.1267222899
2.2222-2.79970.166990.13922287100
2.7997-37.490.1694990.1443236799

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