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- PDB-9f78: BAZ2A bromodomain in complex with acetylpyrrole derivative compou... -

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Basic information

Entry
Database: PDB / ID: 9f78
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 28-TN23
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 / : / 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 / : / 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 / 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
: / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: To Be Published
Title: Unusual backfolded binding poses of BAZ2A bromodomain binders
Authors: Dalle Vedove, A. / Cazzanelli, G. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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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
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4574
Polymers24,7102
Non-polymers7472
Water4,612256
1
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7282
Polymers12,3551
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7282
Polymers12,3551
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.024, 54.360, 90.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / TTF-I-interacting protein 5 / Tip5 / hWALp3


Mass: 12354.839 Da / Num. of mol.: 2 / Mutation: L1848S
Source method: isolated from a genetically manipulated source
Details: Bromodomain (residues 1796-1899). First two residues SM derive from the expression tag. L1848S.
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UIF9
#2: Chemical ChemComp-A1H98 / 1-[4-ethyl-5-[4-[(5-ethyl-1,2,4-oxadiazol-3-yl)methyl]piperazin-1-yl]carbonyl-2-methyl-1~{H}-pyrrol-3-yl]ethanone


Mass: 373.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.35 %
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: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→46.55 Å / Num. obs: 22981 / % possible obs: 96.7 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.079 / Χ2: 0.91 / Net I/σ(I): 12.6 / Num. measured all: 127373
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 93.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.442 / Num. measured all: 6749 / Num. unique obs: 1148 / CC1/2: 0.924 / Rpim(I) all: 0.192 / Rrim(I) all: 0.484 / Χ2: 0.56 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.829 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1158 5.05 %
Rwork0.2088 --
obs0.211 22933 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 54 256 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051849
X-RAY DIFFRACTIONf_angle_d0.8332507
X-RAY DIFFRACTIONf_dihedral_angle_d21.3521116
X-RAY DIFFRACTIONf_chiral_restr0.045245
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.32831220.26522619X-RAY DIFFRACTION94
1.7774-1.87110.30481520.26092625X-RAY DIFFRACTION94
1.8711-1.98830.30431500.24732664X-RAY DIFFRACTION96
1.9883-2.14180.29111480.22992702X-RAY DIFFRACTION96
2.1418-2.35730.28161500.21712766X-RAY DIFFRACTION98
2.3573-2.69840.27461430.2172799X-RAY DIFFRACTION98
2.6984-3.39940.22451480.20282786X-RAY DIFFRACTION97
3.3994-38.8290.21441450.18042814X-RAY DIFFRACTION93
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)
13.9496-0.6878-1.39123.20930.44555.5502-0.2193-0.3529-0.06780.0270.1360.29970.2959-0.54820.06890.1681-0.0335-0.0190.23630.00820.1671-9.8312-7.609724.9452
21.8247-0.3389-2.0112.42720.91857.0888-0.03170.00830.13340.0051-0.022-0.0738-0.1729-0.0040.00580.13110.0159-0.01920.16460.01670.1788-2.3981-3.057226.3783
33.75530.14911.27344.76930.02471.25720.06490.33650.2353-0.3368-0.17010.5411-0.3708-0.81620.13240.25190.0816-0.08210.37490.04290.2633-12.30780.506817.7092
45.2179-0.57-0.42861.7033-0.02544.16830.1745-0.1880.1859-0.0961-0.0801-0.10990.03350.4902-0.06250.17120.0132-0.02070.1667-0.01260.179910.0367-4.94644.1121
53.31530.5717-1.48152.1661-0.07045.62760.0906-0.13860.05050.01140.03370.0112-0.02070.0586-0.10130.08730.0046-0.01360.1317-0.0060.1572.7538-1.407544.1466
64.0151-1.30333.18614.61480.58864.26050.2964-0.40240.6083-0.1702-0.0881-0.9379-0.57111.2235-0.05750.2586-0.1410.07710.3415-0.11010.415614.10264.679748.2714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1797 through 1829 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1830 through 1872 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1873 through 1898 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1796 through 1829 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1830 through 1877 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1878 through 1898 )

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