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- PDB-7bld: BAZ2A bromodomain in complex with compound UZH23 -

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Basic information

Entry
Database: PDB / ID: 7bld
TitleBAZ2A bromodomain in complex with compound UZH23
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-U2K / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G.
Funding support Italy, Switzerland, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
Swiss National Science FoundationSNSF grant 310030B-189363 Switzerland
CitationJournal: to be published
Title: Chemical probes in the BAZ2A bromodomain
Authors: Cazzanelli, G. / Dalle Vedove, A. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
History
DepositionJan 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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)12,9443
Polymers12,3811
Non-polymers5632
Water1,26170
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 area6360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.872, 94.872, 32.539
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 12380.919 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 1796-1899)
Mutation: First two residues SM derive from the expression tag
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-U2K / 1-[3-(6-Methyl-2,3-dihydropyrazolo[5,1-b][1,3]oxazol-7-yl)indol-1-yl]ethanone


Mass: 281.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.41 Å3/Da / Density % sol: 63.98 % / Mosaicity: 0.21 °
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 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.44 Å / Num. obs: 7207 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.078 / Rrim(I) all: 0.26 / Net I/σ(I): 9.8 / Num. measured all: 77949
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
2.35-2.4311.31.61478486930.8160.4991.6911.9100
9.1-47.4410.40.05214921440.9990.0170.05535.599

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimless0.6.2data reduction
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MGJ

5mgj


Resolution: 2.35→31.054 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 346 4.82 %
Rwork0.1902 6835 -
obs0.192 7181 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.78 Å2 / Biso mean: 40.3205 Å2 / Biso min: 15.68 Å2
Refinement stepCycle: final / Resolution: 2.35→31.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 42 70 955
Biso mean--40.27 39.68 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007912
X-RAY DIFFRACTIONf_angle_d0.8021236
X-RAY DIFFRACTIONf_chiral_restr0.046118
X-RAY DIFFRACTIONf_plane_restr0.005158
X-RAY DIFFRACTIONf_dihedral_angle_d14.324525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3503-2.96070.29751800.24783363
2.9607-31.0540.20081660.16943472
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)
13.25980.6713-0.18271.42121.57612.3008-0.0714-0.0415-0.34710.3953-0.0539-0.16140.2919-0.0310.00170.1703-0.05720.00960.401-0.03520.2811-35.887229.8795-14.8381
21.74841.1356-0.70651.53380.87012.6749-0.12270.2139-0.4053-0.23960.0545-0.37120.415-0.05120.00150.2414-0.0920.01590.406-0.06070.3331-29.528928.3651-20.8359
33.0661.27270.30021.61332.03113.1452-0.0677-0.1544-0.4010.42510.1195-0.20620.1005-0.10110.0030.2093-0.0853-0.00570.4018-0.00980.2802-28.048435.0823-9.0986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1797 through 1829 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1830 through 1872 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1873 through 1898 )A0

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