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- PDB-7qz4: BAZ2A bromodomain in complex with acetylpyrrole derivative compound 87 -

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Basic information

Entry
Database: PDB / ID: 7qz4
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 87
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-GIZ / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 30, 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)12,8703
Polymers12,3641
Non-polymers5062
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint3 kcal/mol
Surface area6250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.283, 94.283, 33.091
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: 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-GIZ / 1-[4-ethyl-5-[2-[4-[(1-ethylpiperidin-4-yl)methyl]piperazin-1-yl]-1,3-thiazol-4-yl]-2-methyl-1~{H}-pyrrol-3-yl]ethanone


Mass: 443.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H37N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.43 Å3/Da / Density % sol: 64.18 % / 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: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→81.65 Å / Num. obs: 7731 / % possible obs: 100 % / Redundancy: 18.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.05 / Rrim(I) all: 0.213 / Net I/σ(I): 10.4 / Num. measured all: 139876 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.3-2.3813.51.555103417640.7640.4331.6161.8
8.91-81.65150.11123191550.9940.0310.11625.9

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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: 2.3→47.142 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 395 5.13 %
Rwork0.1838 7304 -
obs0.1858 7699 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.55 Å2 / Biso mean: 53.6528 Å2 / Biso min: 24.88 Å2
Refinement stepCycle: final / Resolution: 2.3→47.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 35 43 920
Biso mean--55.59 49.1 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007901
X-RAY DIFFRACTIONf_angle_d0.9451214
X-RAY DIFFRACTIONf_chiral_restr0.047118
X-RAY DIFFRACTIONf_plane_restr0.005158
X-RAY DIFFRACTIONf_dihedral_angle_d19.62533
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3004-2.63330.28011320.24112396
2.6333-3.31750.2221270.21032427
3.3175-47.1420.20611360.16012481
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)
11.45950.63590.21034.57850.54083.0910.2179-0.65050.61230.1637-0.3234-0.4445-0.64690.1659-0.0560.4668-0.1829-0.02670.6906-0.10480.480534.3988-25.593139.9061
20.4686-0.6816-1.31661.31051.36144.19890.0081-0.0169-0.2789-0.11590.0080.08230.16810.44870.05750.3205-0.04540.00350.56030.00860.383238.5233-37.355722.9148
31.24211.27340.62118.6285.02885.3123-0.13390.1588-0.2021-0.5496-0.0751-0.0636-0.8610.13870.0450.3947-0.1098-0.01890.43630.00220.355129.5273-34.895921.7353
43.45790.6488-1.1962.43281.05164.3448-0.3767-0.21210.4151-0.86020.49980.3947-0.98430.64950.06740.5902-0.2167-0.01350.4988-0.06620.414535.4288-21.877630.631
52.4920.95531.01054.31370.5892.5384-0.22210.02740.50560.0155-0.17710.4972-0.3779-0.14690.26960.3358-0.0583-0.03220.38220.03190.404926.8374-26.60230.9837
64.34090.3352-1.11465.7094-0.44514.76220.1588-0.87080.17770.1271-0.03730.1673-0.33370.4737-0.06770.3356-0.1240.00660.526-0.00480.353127.64-34.39640.2746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1797 through 1818 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1819 through 1829 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1830 through 1839 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1840 through 1848 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1849 through 1872 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1873 through 1898 )A0

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