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- PDB-7qyu: BAZ2A bromodomain in complex with acetylpyrrole derivative compound 88 -

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Basic information

Entry
Database: PDB / ID: 7qyu
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 88
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor 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 / zinc ion binding / nucleus / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-GJC / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 29, 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

Downloads & links

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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)12,8202
Polymers12,3641
Non-polymers4571
Water2,630146
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 area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.127, 35.465, 37.864
Angle α, β, γ (deg.)90.000, 92.490, 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: First two residues SM derive from the expression tag. Double mutant E1845H/L1848S.
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-GJC / 2-[4-[[4-[4-(4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrol-2-yl)-1,3-thiazol-2-yl]piperazin-1-yl]methyl]-1,2,3-triazol-1-yl]ethanamide


Mass: 456.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N8O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.01 Å3/Da / Density % sol: 38.94 % / Mosaicity: 0.3 °
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: 0.9429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9429 Å / Relative weight: 1
ReflectionResolution: 1.5→37.83 Å / Num. obs: 15823 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 15.1 / Num. measured all: 98850 / Scaling rejects: 28
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
1.5-1.5360.73446367790.8940.3240.8042.299
8.22-37.8350.0315451090.9990.0150.03544.796.9

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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: 1.5→27.079 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 683 4.33 %
Rwork0.1588 15107 -
obs0.1602 15790 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.78 Å2 / Biso mean: 24.9865 Å2 / Biso min: 12.87 Å2
Refinement stepCycle: final / Resolution: 1.5→27.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 60 146 1072
Biso mean--33 29.59 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008959
X-RAY DIFFRACTIONf_angle_d1.041303
X-RAY DIFFRACTIONf_chiral_restr0.048126
X-RAY DIFFRACTIONf_plane_restr0.006173
X-RAY DIFFRACTIONf_dihedral_angle_d23.267580
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.61580.25231320.2406298298
1.6158-1.77840.25631980.2059291799
1.7784-2.03570.21321590.173298999
2.0357-2.56440.16651030.14963077100
2.5644-27.0790.1845910.1406314299
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)
10.6358-0.04920.17110.4219-0.39160.44350.0639-0.1288-0.114-0.03380.05490.09380.0102-0.0132-00.19530.0020.00060.1546-0.00080.2226-12.25891.2182-1.0283
21.49560.1554-0.06040.88550.54541.73290.04480.33120.01390.0021-0.02610.00370.00570.06240.00010.18420.02150.00750.18230.00870.17896.19689.6987-7.0395
30.3120.00560.03080.2036-0.26570.27720.0419-0.140.2514-0.01230.05950.169-0.0517-0.06960.00010.2046-0.00790.00770.1428-0.02410.2465-7.35728.56141.54
40.52580.40170.29710.5927-0.16620.5178-0.01820.59340.0683-0.02360.05580.1037-0.0537-0.0292-00.2027-0.00970.00340.24990.02530.1803-4.63910.7861-11.3781
50.6967-0.97910.05191.70980.58951.1871-0.05680.8947-0.5249-0.1351-0.04050.12340.12960.00680.00680.22730.0034-0.00910.3757-0.08890.1594-4.29351.864-15.7274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1794 through 1811 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1812 through 1839 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1840 through 1854 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1855 through 1872 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1873 through 1898 )A0

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