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- PDB-9f6w: BAZ2A bromodomain in complex with acetylpyrrole derivative compou... -

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Basic information

Entry
Database: PDB / ID: 9f6w
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 1-TND14
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 / 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
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: 2.2 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 2, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7144
Polymers12,3641
Non-polymers3503
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-2 kcal/mol
Surface area6220 Å2
Unit cell
Length a, b, c (Å)93.753, 93.753, 33.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: E1845H/L1848S
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag. E1845H/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-A1IAC / 1-(4-ethyl-2-methyl-5-piperazin-1-ylcarbonyl-1~{H}-pyrrol-3-yl)ethanone


Mass: 263.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O2 / 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: 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
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: 3.41 Å3/Da / Density % sol: 63.93 %
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: 0.9997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.2→30.753 Å / Num. obs: 8667 / % possible obs: 99.4 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.047 / Rrim(I) all: 0.203 / Χ2: 0.99 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 98.6 % / Redundancy: 16.8 % / Rmerge(I) obs: 1.587 / Num. measured all: 12232 / Num. unique obs: 726 / CC1/2: 0.846 / Rpim(I) all: 0.396 / Rrim(I) all: 1.637 / Χ2: 1.04 / Net I/σ(I) obs: 2.4

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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: 2.2→30.753 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 431 4.98 %
Rwork0.1696 --
obs0.1707 8655 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→30.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 24 55 939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006913
X-RAY DIFFRACTIONf_angle_d0.7911230
X-RAY DIFFRACTIONf_dihedral_angle_d17.921541
X-RAY DIFFRACTIONf_chiral_restr0.042120
X-RAY DIFFRACTIONf_plane_restr0.004162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.51850.24281420.1892676X-RAY DIFFRACTION99
2.5185-3.17250.21751150.19682758X-RAY DIFFRACTION99
3.1725-30.7530.16921740.1542790X-RAY DIFFRACTION100
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)
13.7124-1.93560.22818.47180.15283.0231-0.0378-0.1811-0.38570.1542-0.3738-0.76420.7051-0.20590.36460.465-0.13850.06170.53280.13070.5165-32.177618.9046-9.5921
21.42680.53471.36531.12760.0653.74150.1331-0.07320.1149-0.0702-0.07030.26470.081-0.8137-0.00610.21120.0028-0.01310.4851-0.02230.3165-37.891936.105-20.5049
31.92361.1572-0.81422.8856-1.54552.3183-0.1787-0.0514-0.3569-0.3928-0.0419-0.34540.3579-0.16150.20030.2843-0.07450.03510.3274-0.0210.3049-29.309227.2999-21.3216
43.97050.61840.70665.559-0.08744.81950.0096-0.5929-0.07370.1636-0.2314-0.18640.0702-0.36620.13080.213-0.0645-0.01350.4583-0.02360.2713-27.111333.7741-9.4489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1795 through 1811 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1812 through 1829 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1830 through 1872 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1873 through 1898 )

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