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- PDB-7qwf: BAZ2A bromodomain in complex with acetylpyrrole derivative compound 45 -

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Basic information

Entry
Database: PDB / ID: 7qwf
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 45
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-FS6 / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: 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.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 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)12,8215
Polymers12,3811
Non-polymers4404
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint1 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.876, 93.876, 33.033
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
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-FS6 / 1-[4-ethyl-2-methyl-5-[2-[2-(methylamino)ethyl]-1,3-thiazol-4-yl]-1~{H}-pyrrol-3-yl]ethanone


Mass: 291.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.39 Å3/Da / Density % sol: 63.76 % / Mosaicity: 0.44 °
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: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.94 Å / Num. obs: 8151 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.047 / Rrim(I) all: 0.154 / Net I/σ(I): 13 / Num. measured all: 86458 / Scaling rejects: 1
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
2.25-2.3211.31.27982917330.8610.3941.3392.4100
9-46.9410.30.03915201470.9980.0130.04146.998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MGJ

5mgj


Resolution: 2.25→40.65 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 326 4.01 %
Rwork0.199 7796 -
obs0.2006 8122 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.08 Å2 / Biso mean: 57.8537 Å2 / Biso min: 21.24 Å2
Refinement stepCycle: final / Resolution: 2.25→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 29 55 945
Biso mean--56.37 49.16 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007919
X-RAY DIFFRACTIONf_angle_d0.9021235
X-RAY DIFFRACTIONf_chiral_restr0.045121
X-RAY DIFFRACTIONf_plane_restr0.005162
X-RAY DIFFRACTIONf_dihedral_angle_d21.149343
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2503-2.8350.30821690.26883839
2.835-40.650.21651570.17713957
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)
13.5723-2.6829-3.29512.25911.80766.0717-0.3418-0.7645-1.04480.2156-0.06810.04590.90070.18350.35070.5493-0.33480.00280.80010.15120.7857-31.883118.52167.177
20.7390.4001-1.28692.8138-1.00212.31840.04680.1643-0.2545-0.4421-0.07030.10010.5255-1.10390.0210.3273-0.164-0.03630.9735-0.02340.4141-33.957730.088-5.4914
34.20631.4432-0.083.25981.10974.23630.2455-0.3697-0.47220.2297-0.23-0.33420.1148-0.6137-0.04130.2925-0.1431-0.01970.61060.01830.3316-26.565532.08363.8036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1795 through 1810 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1811 through 1854 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1855 through 1898 )A0

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