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- PDB-7qvv: BAZ2A bromodomain in complex with pyridone derivative fragment 36 -

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Basic information

Entry
Database: PDB / ID: 7qvv
TitleBAZ2A bromodomain in complex with pyridone derivative fragment 36
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 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FI9 / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.601 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 23, 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)12,6022
Polymers12,3811
Non-polymers2211
Water37821
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 area6160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.446, 91.446, 32.627
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-FI9 / 5-(4-azanylpiperidin-1-yl)carbonyl-1~{H}-pyridin-2-one


Mass: 221.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.18 Å3/Da / Density % sol: 61.33 % / Mosaicity: 0.6 °
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: 2.6→45.72 Å / Num. obs: 5008 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.069 / Rrim(I) all: 0.221 / Net I/σ(I): 10.6 / Num. measured all: 50649
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
2.6-2.729.81.40860126110.6610.4711.4862100
9.01-45.72100.05813741380.9980.020.0622998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MGJ

5mgj


Resolution: 2.601→30.167 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 234 4.68 %
Rwork0.2259 4764 -
obs0.2275 4998 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.64 Å2 / Biso mean: 53.7712 Å2 / Biso min: 18.48 Å2
Refinement stepCycle: final / Resolution: 2.601→30.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 16 21 890
Biso mean--43.44 36.6 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006899
X-RAY DIFFRACTIONf_angle_d1.0881213
X-RAY DIFFRACTIONf_chiral_restr0.056121
X-RAY DIFFRACTIONf_plane_restr0.007160
X-RAY DIFFRACTIONf_dihedral_angle_d16.48534
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.601-3.27580.34711080.27412366
3.2758-30.1670.23051260.20432398
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)
12.89340.6899-0.3211.9353-0.46461.12010.2043-0.357-0.68920.2415-0.4315-0.09330.09420.1015-0.05430.3082-0.243-0.07530.78180.06040.4855-34.467127.25691.5142
22.34821.20010.0692.6827-0.55391.0170.07290.0377-0.6602-0.17910.1483-0.03920.4046-0.3721-0.13430.405-0.308-0.00940.7394-0.02540.4191-28.386926.3458-4.5275
33.80280.8435-0.61271.58421.62412.31490.1478-0.2977-0.40060.1942-0.2406-0.16070.14590.05850.08560.3429-0.272-0.05480.85850.10110.2654-26.514132.84067.1296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1796 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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